Yes, desecrating multiple altars gives diminishing returns - and this is in large part due to Naga City and GT antics. Same reason altars in Naga City require gold to unlock. It's just one of those things that are obscure due to the way gods are introduced to the game.

Really, the more you play vicious dungeons (and the whole game) the faster you can get through them. It takes me a very short amount of time now (5-10 minutes, depending on dungeon and simplicity of strategy), but my first vicious took me forever. It really depends on how much you have to focus on all the possible resources you have.